X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details 9.5 - 10 % PEG 3K, 100 MM KCL, 200 MM MGCL2, 40 MM SODIUM CACODYLATE PH 5.5, 5 MM DTT.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 183.31 α = 90
b = 183.31 β = 90
c = 111.28 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC COMPOUND REFRACTIVE LENSES 2010-10-01
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 -- DIAMOND I04

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.27 70.75 99.9 0.08 -- -- 9.2 -- 29895 -- -- 106.14
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.27 3.35 100.0 0.75 -- 2.8 9.5 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
OTHER 3.269 53.56 -- 1.35 -- 29852 3776 99.88 -- 0.2246 0.2205 0.2813 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.2694 3.3108 -- 136 1932 0.386 0.4561 -- 100.0
X Ray Diffraction 3.3108 3.3543 -- 142 1952 0.3542 0.3886 -- 100.0
X Ray Diffraction 3.3543 3.4003 -- 140 1935 0.3357 0.4048 -- 100.0
X Ray Diffraction 3.4003 3.4488 -- 132 1920 0.3231 0.4199 -- 100.0
X Ray Diffraction 3.4488 3.5003 -- 141 1928 0.309 0.3462 -- 100.0
X Ray Diffraction 3.5003 3.555 -- 138 1930 0.2925 0.3833 -- 100.0
X Ray Diffraction 3.555 3.6133 -- 135 1941 0.301 0.3811 -- 100.0
X Ray Diffraction 3.6133 3.6756 -- 137 1941 0.2923 0.4127 -- 100.0
X Ray Diffraction 3.6756 3.7424 -- 138 1931 0.2523 0.2816 -- 100.0
X Ray Diffraction 3.7424 3.8143 -- 142 1936 0.2373 0.3365 -- 100.0
X Ray Diffraction 3.8143 3.8922 -- 139 1931 0.2372 0.3258 -- 100.0
X Ray Diffraction 3.8922 3.9768 -- 144 1941 0.2345 0.3114 -- 100.0
X Ray Diffraction 3.9768 4.0693 -- 137 1916 0.2136 0.2713 -- 100.0
X Ray Diffraction 4.0693 4.171 -- 140 1951 0.197 0.26 -- 100.0
X Ray Diffraction 4.171 4.2837 -- 141 1944 0.2223 0.2778 -- 100.0
X Ray Diffraction 4.2837 4.4097 -- 137 1906 0.2168 0.2915 -- 100.0
X Ray Diffraction 4.4097 4.552 -- 141 1949 0.2064 0.3113 -- 100.0
X Ray Diffraction 4.552 4.7146 -- 141 1942 0.2043 0.2509 -- 100.0
X Ray Diffraction 4.7146 4.9032 -- 140 1906 0.2113 0.3168 -- 100.0
X Ray Diffraction 4.9032 5.1262 -- 140 1947 0.2264 0.2865 -- 100.0
X Ray Diffraction 5.1262 5.3962 -- 144 1938 0.2476 0.338 -- 100.0
X Ray Diffraction 5.3962 5.7339 -- 143 1916 0.2648 0.3227 -- 100.0
X Ray Diffraction 5.7339 6.1761 -- 142 1947 0.2273 0.3426 -- 100.0
X Ray Diffraction 6.1761 6.7965 -- 142 1930 0.2138 0.2419 -- 100.0
X Ray Diffraction 6.7965 7.7774 -- 137 1943 0.1676 0.2184 -- 100.0
X Ray Diffraction 7.7774 9.7889 -- 144 1915 0.138 0.1756 -- 99.0
X Ray Diffraction 9.7889 53.5673 -- 143 1923 0.1944 0.2251 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 103.54
Anisotropic B[1][1] -15.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -15.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 31.4801
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.01
f_plane_restr 0.004
f_angle_d 1.279
f_chiral_restr 0.083
f_dihedral_angle_d 20.198
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11807
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 8

Software

Computing
Computing Package Purpose
XIA2, XDS Data Reduction (intensity integration)
XIA2, SCALA Data Reduction (data scaling)
SNB, AUTOSHARP, PHENIX AUTOBUILD, COOT, PHENIX.REFINE, PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: AUTOBUILD model building
PHENIX.REFINE model building
PHENIX version: (PHENIX.REFINE) refinement
SNB model building
COOT model building
AUTOSHARP model building
PHASER model building